This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

Metagenomic biomarker discovery and explanation

The alpha diversity of ecologic communities is affected by many biotic and abiotic drivers and, in turn, affects ecosystem functioning. Yet, patterns of alpha diversity in host-associated microbial communities (microbiomes) are poorly studied and the appropriateness of general theory is untested. Expanding diversity theory to include microbiomes is essential as diversity is a frequently cited metric of their status. Here, we review and newly analyze reports of alpha diversity for animal gut microbiomes. We demonstrate that both diet and body size affect diversity in the gut but that gut physiology (fermenter versus simple) is the most important driver. We also assess the advantages of various diversity metrics. The importance of diversity in microbiomes is often assumed but has not been tested outright. Therefore, we close by discussing how to integrate microbiomes into the field of biodiversity-ecosystem functioning to more clearly understand when and why a host supports diverse microbial communities.

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance.

This review summarizes the key results of recently published studies on the effects of dietary change and nutritional intervention on the human microbiome from around the world, focusing on the USA, Canada, Europe, Asia, and Africa. It first explores mechanisms that might explain the ability of fiber-rich foods to suppress the incidence and mortality from westernized diseases, notably cancers of the colon, breast, liver, cardiovascular, infectious, and respiratory diseases, diabetes, and obesity (O’Keefe in Lancet Gastroenterol Hepatol 4(12):984–996, 2019; Am J Clin Nutr 110:265–266, 2019). It summarizes studies from Africa which suggest that disturbance of the colonic microbiome may exacerbate chronic malnutrition and growth failure in impoverished communities and highlights the importance of breast feeding. The American section discusses the role of the microbiome in the swelling population of patients with obesity and type 2 diabetes and examines the effects of race, ethnicity, geography, and climate on microbial diversity and metabolism. The studies from Europe and Asia extoll the benefits of whole foods and plant-based diets. The Asian studies examine the worrying changes from low-fat, high-carbohydrate diets to high-fat, low-carbohydrate ones and the increasing appearance of westernized diseases as in Africa and documents the ability of high-fiber traditional Chinese diets to reverse type 2 diabetes and control weight loss. In conclusion, most of the studies reviewed demonstrate clear changes in microbe abundances and in the production of fermentation products, such as short-chain fatty acids and phytochemicals following dietary change, but the significance of the microbiota changes to human health, with the possible exception of the stimulation of butyrogenic taxa by fiber-rich foods, is generally implied and not measured. Further studies are needed to determine how these changes in microbiota composition and metabolism can improve our health and be used to prevent and treat disease.

Diet and the Human Gut Microbiome: An International Review

The gut microbiota has a profound impact on human health. Emerging data show that dietary patterns are associated with different communities of bacterial species within the gut. Prevotella species have been correlated with plant-rich diets, abundant in carbohydrates and fibres. Dysbiosis within the gut ecosystem has been associated with the development of non-communicable diseases such as obesity, the metabolic syndrome, inflammatory bowel disease, irritable bowel syndrome, colorectal cancer, type 1 diabetes, allergies and other diseases. The purpose of this comprehensive literature review was to evaluate the available data on the impact of diet on the Prevotella genus, as a dietary fibre fermenter in the gut as well as its implications as a potential biomarker for homeostasis or disease state through its metabolite signature. Studies were identified by conducting PubMed, Web of Science Core Collection and Google Scholar electronic searches. We found eighty-five publications reporting the impact of dietary patterns on gut microbial communities, including Prevotella or Prevotella/Bacteroides ratio in particular. Moreover, the role of Prevotella species on health status was also evaluated. Prevotella possess a high genetic diversity, representing one of the important groups found in the oral cavity and large intestine of man. The gut commensal Prevotella bacteria contribute to polysaccharide breakdown, being dominant colonisers of agrarian societies. However, studies also suggested a potential role of Prevotella species as intestinal pathobionts. Further metagenomic studies are needed in order to reveal health- or disease-modulating properties of Prevotella species in the gut.

Gut Prevotella as a possible biomarker of diet and its eubiotic versus dysbiotic roles: a comprehensive literature review.

The human microbiome has been associated with health status, and risk of disease development. While the etiology of microbiome-mediated disease remains to be fully elucidated, one mechanism may be through microbial metabolism. Metabolites produced by commensal organisms, including in response to host diet, may affect host metabolic processes, with potentially protective or pathogenic consequences. We conducted multi-omic phenotyping of healthy subjects (N = 136), in order to investigate the interaction between diet, the microbiome, and the metabolome in a cross-sectional sample. We analyzed the nutrient composition of self-reported diet (3-day food records and food frequency questionnaires). We profiled the gut and oral microbiome (16S rRNA) from stool and saliva, and applied metabolomic profiling to plasma and stool samples in a subset of individuals (N = 75). We analyzed these multi-omic data to investigate the relationship between diet, the microbiome, and the gut and circulating metabolome. On a global level, we observed significant relationships, particularly between long-term diet, the gut microbiome and the metabolome. Intake of plant-derived nutrients as well as consumption of artificial sweeteners were associated with significant differences in circulating metabolites, particularly bile acids, which were dependent on gut enterotype, indicating that microbiome composition mediates the effect of diet on host physiology. Our analysis identifies dietary compounds and phytochemicals that may modulate bacterial abundance within the gut and interact with microbiome composition to alter host metabolism.

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Multi-Omic Analysis of the Microbiome and Metabolome in Healthy Subjects Reveals Microbiome-Dependent Relationships Between Diet and Metabolites

The human gut microbiome represents a diverse microbial community that varies across individuals and populations, and is influenced by factors such as host genetics and lifestyle. Diet is a major force shaping the gut microbiome, and the effects of dietary choices on microbiome composition are well documented. However, it remains poorly known how natural temporal variation in diet can affect the microbiome. The traditional Inuit diet is primarily based on animal products, which are thought to vary seasonally according to prey availability. We previously investigated the Inuit gut microbiome sampled at a single time point, and found no detectable differences in overall microbiome community composition attributable to the traditional Inuit diet. To determine whether seasonal changes in the Inuit diet might induce more pronounced changes in the microbiome, we collected stool and toilet paper samples, and dietary information from Inuit volunteers living in Resolute Bay (Nunavut, Canada), and compared them to individuals of European descent living in Montreal (Quebec, Canada) consuming a typical Western diet. We sequenced the V4 region of the 16S rRNA gene to characterize microbiome diversity and composition, and compared samples collected with toilet paper or from stool. Our results show that these sampling methods provide similar, but non-identical portraits of the microbiome. Based on toilet paper samples, we found that much of the variation in microbiome community composition could be explained by individual identity (45–61% of variation explained, depending on the beta diversity metric used), with small but significant variation (3–5%) explained by sex or geography (Nunavut or Montreal). In contrast with our previous study at one time point, sampling over the course of a year revealed that diet explains 11% of variation in community composition across all participants, and 17% of variation specifically among Nunavut participants. However, we observed no clear seasonal shifts in the microbiomes of participants from either Nunavut or Montreal. Within-individual microbial diversity fluctuated more over time in Nunavut than in Montreal, consistent with a more variable and highly individualized diet in Nunavut. Together, these results shows that the traditional Inuit diet and lifestyle has an impact on the composition, diversity and stability of the Inuit gut microbiome, even if the seasonality of the diet is less pronounced than expected, perhaps due to an increasingly westernized diet.

/pdf/the-inuit-gut-microbiome-is-dynamic-over-time-and-shaped-by-4c09b7idn8.pdf

The Inuit gut microbiome is dynamic over time and shaped by traditional foods

New records of the Southern Flying Squirrel ( Glaucomys volans ) in Quebec expand its known range in the province 150 km east to the appalachian foothills and farther west than previously assumed. We obtained individuals through live trapping, trapper collaboration, and opportunistic discoveries. Species identification was confirmed with morphological traits and molecular analysis. individuals were smaller in the eastern part of the province in terms of mass, total length, and tail length. Some live captures also seem to corroborate the fact that Southern Flying Squirrels are mainly associated with mature hardwood forests. De nouvelles mentions du petit polatouche ( Glaucomys volans ) au Quebec permettent d’etendre son aire de repartition connue jusqu’a 150 km a l’est dans les contreforts des appalaches et plus a l’ouest que presume. Les specimens ont ete obtenus via des captures vivantes, la collaboration des trappeurs et des decouvertes opportunistes. L’identification de l’espece a ete confirmee sur des bases morphologiques et moleculaires. Les individus etaient plus petits dans l’est de la province en considerant la masse, la longueur totale et celle de la queue. Les quelques captures d’animaux vivants semblent corroborer que le petit polatouche est davantage associe, au niveau de l’habitat, aux peuplements de feuillus matures.

http://www.canadianfieldnaturalist.ca/index.php/cfn/article/download/1883/1826

Known Range Expansion and Morphological Variation in the Southern Flying Squirrel ( Glaucomys volans ) in Quebec

The two species of flying squirrels found in North America are the northern (Glaucomys sabrinus) and the southern (G. volans) flying squirrel. Both species have wide range distributions across North America, yet differences in their preferred habitat result in few areas of sympatry. Climate change however, has shifted the southern flying squirrel’s range limit further north, thus allowing the two species to encounter each other more frequently. Glaucomys volans is the more competitive of the two, and also carries a nematode parasite (Strongyloides robustus) proven to be deleterious towards its sister species. The northern incursion of the southern flying squirrel may therefore dislodge its sister species from its original distribution. With G. sabrinus considered endangered in different parts of North America, and G. volans listed as “concerned” in its northernmost limit, the two species require close monitoring. Morphological identification is often challenging for incomplete and juvenile specimens, therefore we developed a molecular identification protocol using mitochondrial and nuclear markers in tandem to help distinguish each species. These protocols were tested on Glaucomys individuals located elsewhere in Canada and the USA to ensure the validity of the designed primers. Moreover, employing our methods may detect F1 hybrids. To assess the current genetic portrait of G. sabrinus populations in Quebec before the potential invasion of its sister species, a preliminary population genetics study using seven microsatellite loci was also realized. The various conservation and management implications are discussed.

Geneviève Dubois

Papers

The Inuit gut microbiome is dynamic over time and shaped by traditional foods

Known Range Expansion and Morphological Variation in the Southern Flying Squirrel ( Glaucomys volans ) in Quebec

Applying genetic methods to identify northern and southern flying squirrels and determine conservation needs